
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   23 (   92),  selected   23 , name T0358AL381_3-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   23 , name T0358_D1.pdb
# PARAMETERS: T0358AL381_3-D1.T0358_D1.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23        35 - 57          2.02     2.02
  LCS_AVERAGE:     35.38

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22        35 - 56          1.88     2.07
  LONGEST_CONTINUOUS_SEGMENT:    22        36 - 57          1.98     2.05
  LCS_AVERAGE:     33.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        35 - 43          0.85     2.37
  LONGEST_CONTINUOUS_SEGMENT:     9        47 - 55          0.62     2.51
  LCS_AVERAGE:     12.71

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   65
LCS_GDT     S      35     S      35      9   22   23     3   10   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     H      36     H      36      9   22   23     3   10   14   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     F      37     F      37      9   22   23     3   10   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      38     R      38      9   22   23     4   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      39     L      39      9   22   23     9   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      40     V      40      9   22   23     9   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      41     V      41      9   22   23     9   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      42     R      42      9   22   23     9   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     D      43     D      43      9   22   23     4   10   15   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     T      44     T      44      7   22   23     3    7   12   17   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      45     E      45      7   22   23     3    9   14   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     G      46     G      46      8   22   23     4    5   11   15   18   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      47     R      47      9   22   23     6   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     M      48     M      48      9   22   23     9   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     V      49     V      49      9   22   23     9   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     W      50     W      50      9   22   23     9   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      51     R      51      9   22   23     9   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     A      52     A      52      9   22   23     6   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     W      53     W      53      9   22   23     8   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     N      54     N      54      9   22   23     9   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     F      55     F      55      9   22   23     7   13   16   18   19   20   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      56     E      56      3   22   23     3    3    3    4    5   15   20   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     P      57     P      57      3   22   23     0    3    6   12   18   19   22   23   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_AVERAGE  LCS_A:  27.31  (  12.71   33.85   35.38 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      9     13     16     18     19     20     22     23     23     23     23     23     23     23     23     23     23     23     23     23 
GDT PERCENT_CA  13.85  20.00  24.62  27.69  29.23  30.77  33.85  35.38  35.38  35.38  35.38  35.38  35.38  35.38  35.38  35.38  35.38  35.38  35.38  35.38
GDT RMS_LOCAL    0.33   0.53   0.95   1.14   1.29   1.43   1.85   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02
GDT RMS_ALL_CA   2.57   2.64   2.58   2.42   2.29   2.24   2.04   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02

#      Molecule1      Molecule2       DISTANCE
LGA    S      35      S      35          2.377
LGA    H      36      H      36          2.506
LGA    F      37      F      37          1.682
LGA    R      38      R      38          0.738
LGA    L      39      L      39          0.687
LGA    V      40      V      40          0.609
LGA    V      41      V      41          0.581
LGA    R      42      R      42          0.476
LGA    D      43      D      43          1.764
LGA    T      44      T      44          3.865
LGA    E      45      E      45          3.522
LGA    G      46      G      46          2.761
LGA    R      47      R      47          0.863
LGA    M      48      M      48          1.062
LGA    V      49      V      49          0.809
LGA    W      50      W      50          0.583
LGA    R      51      R      51          1.001
LGA    A      52      A      52          1.568
LGA    W      53      W      53          1.696
LGA    N      54      N      54          2.109
LGA    F      55      F      55          2.251
LGA    E      56      E      56          3.998
LGA    P      57      P      57          3.552

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23   65    4.0     23    2.02    29.615    31.667     1.085

LGA_LOCAL      RMSD =  2.020  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.107  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  2.020  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.716062 * X  +  -0.670175 * Y  +   0.195242 * Z  +  25.468029
  Y_new =   0.690204 * X  +  -0.721551 * Y  +   0.054618 * Z  +  14.145958
  Z_new =   0.104274 * X  +   0.173866 * Y  +   0.979233 * Z  + -65.970078 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.175722   -2.965870  [ DEG:    10.0682   -169.9319 ]
  Theta =  -0.104464   -3.037129  [ DEG:    -5.9853   -174.0147 ]
  Phi   =   2.374580   -0.767012  [ DEG:   136.0534    -43.9466 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0358AL381_3-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358AL381_3-D1.T0358_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23   65   4.0   23   2.02  31.667     2.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL381_3-D1
REMARK Aligment from pdb entry: 1m93C
ATOM      1  N   SER    35       6.645  10.144  -6.195  1.00  0.00              
ATOM      2  CA  SER    35       5.973  11.390  -5.802  1.00  0.00              
ATOM      3  C   SER    35       4.721  10.978  -4.998  1.00  0.00              
ATOM      4  O   SER    35       4.443   9.777  -4.973  1.00  0.00              
ATOM      5  N   HIS    36       4.058  11.870  -4.275  1.00  0.00              
ATOM      6  CA  HIS    36       3.060  11.426  -3.278  1.00  0.00              
ATOM      7  C   HIS    36       1.995  10.502  -3.840  1.00  0.00              
ATOM      8  O   HIS    36       1.466  10.680  -4.949  1.00  0.00              
ATOM      9  N   PHE    37       1.674   9.475  -3.047  1.00  0.00              
ATOM     10  CA  PHE    37       0.729   8.471  -3.496  1.00  0.00              
ATOM     11  C   PHE    37      -0.138   8.002  -2.332  1.00  0.00              
ATOM     12  O   PHE    37       0.181   8.291  -1.175  1.00  0.00              
ATOM     13  N   ARG    38      -1.223   7.311  -2.644  1.00  0.00              
ATOM     14  CA  ARG    38      -2.050   6.705  -1.607  1.00  0.00              
ATOM     15  C   ARG    38      -1.923   5.199  -1.671  1.00  0.00              
ATOM     16  O   ARG    38      -1.730   4.610  -2.750  1.00  0.00              
ATOM     17  N   LEU    39      -1.981   4.527  -0.524  1.00  0.00              
ATOM     18  CA  LEU    39      -1.857   3.080  -0.508  1.00  0.00              
ATOM     19  C   LEU    39      -2.956   2.549   0.431  1.00  0.00              
ATOM     20  O   LEU    39      -3.248   3.187   1.464  1.00  0.00              
ATOM     21  N   VAL    40      -3.544   1.428   0.023  1.00  0.00              
ATOM     22  CA  VAL    40      -4.638   0.776   0.734  1.00  0.00              
ATOM     23  C   VAL    40      -4.313  -0.692   0.984  1.00  0.00              
ATOM     24  O   VAL    40      -3.988  -1.368  -0.006  1.00  0.00              
ATOM     25  N   VAL    41      -4.395  -1.145   2.237  1.00  0.00              
ATOM     26  CA  VAL    41      -4.296  -2.580   2.508  1.00  0.00              
ATOM     27  C   VAL    41      -5.712  -3.136   2.622  1.00  0.00              
ATOM     28  O   VAL    41      -6.527  -2.642   3.408  1.00  0.00              
ATOM     29  N   ARG    42      -6.046  -4.144   1.809  1.00  0.00              
ATOM     30  CA  ARG    42      -7.438  -4.586   1.870  1.00  0.00              
ATOM     31  C   ARG    42      -7.558  -6.101   1.712  1.00  0.00              
ATOM     32  O   ARG    42      -6.644  -6.777   1.234  1.00  0.00              
ATOM     33  N   ASP    43      -8.722  -6.579   2.130  1.00  0.00              
ATOM     34  CA  ASP    43      -9.103  -7.969   1.921  1.00  0.00              
ATOM     35  C   ASP    43      -9.561  -8.091   0.473  1.00  0.00              
ATOM     36  O   ASP    43     -10.348  -7.273  -0.019  1.00  0.00              
ATOM     37  N   THR    44      -9.064  -9.081  -0.267  1.00  0.00              
ATOM     38  CA  THR    44      -9.464  -9.047  -1.684  1.00  0.00              
ATOM     39  C   THR    44     -10.922  -9.486  -1.740  1.00  0.00              
ATOM     40  O   THR    44     -11.387 -10.359  -1.013  1.00  0.00              
ATOM     41  N   GLU    45     -11.654  -8.787  -2.601  1.00  0.00              
ATOM     42  CA  GLU    45     -13.108  -8.912  -2.613  1.00  0.00              
ATOM     43  C   GLU    45     -13.720  -8.418  -1.318  1.00  0.00              
ATOM     44  O   GLU    45     -14.872  -8.617  -0.928  1.00  0.00              
ATOM     45  N   GLY    46     -12.960  -7.681  -0.508  1.00  0.00              
ATOM     46  CA  GLY    46     -13.549  -7.313   0.776  1.00  0.00              
ATOM     47  C   GLY    46     -13.142  -5.930   1.247  1.00  0.00              
ATOM     48  O   GLY    46     -12.930  -4.949   0.548  1.00  0.00              
ATOM     49  N   ARG    47     -13.041  -5.861   2.567  1.00  0.00              
ATOM     50  CA  ARG    47     -12.977  -4.567   3.193  1.00  0.00              
ATOM     51  C   ARG    47     -11.562  -4.003   3.216  1.00  0.00              
ATOM     52  O   ARG    47     -10.542  -4.665   3.170  1.00  0.00              
ATOM     53  N   MET    48     -11.578  -2.687   3.308  1.00  0.00              
ATOM     54  CA  MET    48     -10.371  -1.918   3.591  1.00  0.00              
ATOM     55  C   MET    48      -9.893  -2.048   5.018  1.00  0.00              
ATOM     56  O   MET    48     -10.612  -1.826   5.999  1.00  0.00              
ATOM     57  N   VAL    49      -8.638  -2.418   5.149  1.00  0.00              
ATOM     58  CA  VAL    49      -8.050  -2.653   6.471  1.00  0.00              
ATOM     59  C   VAL    49      -7.233  -1.454   6.956  1.00  0.00              
ATOM     60  O   VAL    49      -7.302  -1.075   8.131  1.00  0.00              
ATOM     61  N   TRP    50      -6.465  -0.846   6.051  1.00  0.00              
ATOM     62  CA  TRP    50      -5.618   0.310   6.377  1.00  0.00              
ATOM     63  C   TRP    50      -5.566   1.195   5.134  1.00  0.00              
ATOM     64  O   TRP    50      -5.713   0.677   4.017  1.00  0.00              
ATOM     65  N   ARG    51      -5.365   2.483   5.320  1.00  0.00              
ATOM     66  CA  ARG    51      -5.285   3.402   4.177  1.00  0.00              
ATOM     67  C   ARG    51      -4.286   4.488   4.573  1.00  0.00              
ATOM     68  O   ARG    51      -4.321   4.976   5.725  1.00  0.00              
ATOM     69  N   ALA    52      -3.392   4.841   3.656  1.00  0.00              
ATOM     70  CA  ALA    52      -2.379   5.841   3.985  1.00  0.00              
ATOM     71  C   ALA    52      -2.035   6.731   2.809  1.00  0.00              
ATOM     72  O   ALA    52      -2.355   6.449   1.654  1.00  0.00              
ATOM     73  N   TRP    53      -1.383   7.858   3.140  1.00  0.00              
ATOM     74  CA  TRP    53      -0.784   8.753   2.179  1.00  0.00              
ATOM     75  C   TRP    53       0.712   8.754   2.455  1.00  0.00              
ATOM     76  O   TRP    53       1.144   8.986   3.608  1.00  0.00              
ATOM     77  N   ASN    54       1.482   8.496   1.407  1.00  0.00              
ATOM     78  CA  ASN    54       2.937   8.639   1.452  1.00  0.00              
ATOM     79  C   ASN    54       3.246  10.035   0.881  1.00  0.00              
ATOM     80  O   ASN    54       3.148  10.217  -0.343  1.00  0.00              
ATOM     81  N   PHE    55       3.673  10.954   1.726  1.00  0.00              
ATOM     82  CA  PHE    55       3.996  12.321   1.336  1.00  0.00              
ATOM     83  C   PHE    55       5.492  12.580   1.311  1.00  0.00              
ATOM     84  O   PHE    55       5.990  13.419   0.559  1.00  0.00              
ATOM     85  N   GLU    56       6.198  11.856   2.198  1.00  0.00              
ATOM     86  CA  GLU    56       7.622  12.126   2.343  1.00  0.00              
ATOM     87  C   GLU    56       8.334  10.975   3.056  1.00  0.00              
ATOM     88  O   GLU    56       7.799  10.295   3.933  1.00  0.00              
ATOM     89  N   PRO    57       9.573  10.807   2.624  1.00  0.00              
ATOM     90  CA  PRO    57      10.515   9.880   3.269  1.00  0.00              
ATOM     91  C   PRO    57      10.767  10.231   4.726  1.00  0.00              
ATOM     92  O   PRO    57      10.962  11.414   5.045  1.00  0.00              
END
